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That just tells FFmpeg to copy the video and audio streams but put them in a new mp4 format (the -f option).
The resultant mp4 still has the same AVC/AC3 combination but now in a MP4 wrapper.

I played both source and output in VLC and they looked the same - obviously you should satisfy yourself that quality has been maintained.
I'll wager that most GUI tools to do this task use FFmpeg under the hood.